In 2012 we discovered an African American customer sample that didn’t match any known Y haplogroup. Our further investigation showed that he represented a new Y branch (A00) predating all other known haplogroups by at least 70,000 years. Research in public Y-STR databases indicated that the haplotype of the A00 sample was found in Cameroon.

Methods

We sequenced the Y chromosome of this sample with classical Sanger technology (ABI3730XL, ~400,000 bases) to identify the general structure of the new branch and established SNP typing assays for a selection of key markers that could be used to screen a wider population. We collected 950 male cheek swab samples in different regions of Cameroon and intensified the sampling density in regions where A00 was found. Later we sequenced four A00 samples with NGS technology (Illumina HiSeq X Ten) to elaborate 3 distinct branches within A00.

Results

We found 5018 novel Y-SNPs on the A00 branch, 1455 Y-SNPs on the A0-T branch. The screening identified 83 samples that we confirmed to belong to haplogroup A00-L1086. Every confirmed A00 sample could be assigned to one of the 3 branches A00a A00b and A00c defined by the markers FGC25576, A4985 and A12222 respectively.

Conclusions

We observed a very restricted regional distribution of the A00 population and a very young TMRCA of 700 ybp despite the extremely deep split from all other known Y haplogroups of more than 200,000 ybp. A00 is significantly older than the previously oldest branch A0-V148. And the A00 population is tightly concentrated in the mountains of West Cameroon. The highest A00 frequency is observed among the Bangwa and Mbo while we didn’t observe any A00 samples among the Baka people who were suspected to be distinct from their visual appearance and language.